The "extraordinary rendition" program the CIA was using to disappear terror suspects into places they could be tortured was discovered in part by airplane-spotting hobbyists. Because planes are extremely hard to hide, and there are people who watch airports to see what takes off and lands for fun.
When they pooled their data, they were the first group to notice the military had started running flights to and from locations they didn't normally fly, and it didn't take much investigative journalism after that to discover those planes were carrying people.